void MDHistoToWorkspace2D::exec() {
IMDHistoWorkspace_sptr inWS =
IMDHistoWorkspace_sptr(getProperty("InputWorkspace"));
rank = inWS->getNumDims();
size_t nSpectra = calculateNSpectra(inWS);
std::cout << "nSpectra = " << nSpectra << std::endl;
boost::shared_ptr<const IMDDimension> lastDim = inWS->getDimension(rank - 1);
std::cout << "spectraLength = " << lastDim->getNBins() << std::endl;
Mantid::DataObjects::Workspace2D_sptr outWS;
outWS = boost::dynamic_pointer_cast<Mantid::DataObjects::Workspace2D>(
WorkspaceFactory::Instance().create(
"Workspace2D", nSpectra, lastDim->getNBins(), lastDim->getNBins()));
outWS->setYUnit("Counts");
coord_t *pos = (coord_t *)malloc(rank * sizeof(coord_t));
memset(pos, 0, rank * sizeof(coord_t));
currentSpectra = 0;
recurseData(inWS, outWS, 0, pos);
copyMetaData(inWS, outWS);
// checkW2D(outWS);
setProperty("OutputWorkspace", boost::dynamic_pointer_cast<Workspace>(outWS));
}
void
MDHistoToWorkspace2D::checkW2D(Mantid::DataObjects::Workspace2D_sptr outWS) {
size_t nSpectra = outWS->getNumberHistograms();
size_t length = outWS->blocksize();
MantidVec x, y, e;
g_log.information() << "W2D has " << nSpectra << " histograms of length "
<< length;
for (size_t i = 0; i < nSpectra; i++) {
ISpectrum *spec = outWS->getSpectrum(i);
x = spec->dataX();
y = spec->dataY();
e = spec->dataE();
if (x.size() != length) {
g_log.information() << "Spectrum " << i << " x-size mismatch, is "
<< x.size() << " should be " << length << "\n";
}
if (y.size() != length) {
g_log.information() << "Spectrum " << i << " y-size mismatch, is "
<< y.size() << " should be " << length << "\n";
}
if (e.size() != length) {
g_log.information() << "Spectrum " << i << " e-size mismatch, is "
<< e.size() << " should be " << length << "\n";
}
}
}
void MDHistoToWorkspace2D::copyMetaData(
Mantid::API::IMDHistoWorkspace_sptr inWS,
Mantid::DataObjects::Workspace2D_sptr outWS) {
if (inWS->getNumExperimentInfo() > 0) {
ExperimentInfo_sptr info = inWS->getExperimentInfo(0);
outWS->copyExperimentInfoFrom(info.get());
}
outWS->setTitle(inWS->getTitle());
}
/**
* Populate spectra mapping to detector IDs
*
* @param workspace: Workspace2D object
* @param nxbins: number of bins in X
* @param nybins: number of bins in Y
*/
void SANSInstrumentCreationHelper::runLoadMappingTable(
Mantid::DataObjects::Workspace2D_sptr workspace, int nxbins, int nybins) {
// Get the number of monitor channels
size_t nMonitors(0);
size_t nXbins, nYbins;
boost::shared_ptr<const Instrument> instrument = workspace->getInstrument();
std::vector<detid_t> monitors = instrument->getMonitors();
nMonitors = monitors.size();
// Number of monitors should be consistent with data file format
if (nMonitors != 2) {
std::stringstream error;
error << "Geometry error for " << instrument->getName()
<< ": Spice data format defines 2 monitors, " << nMonitors
<< " were/was found";
throw std::runtime_error(error.str());
}
if (nxbins >= 0) {
nXbins = size_t(nxbins);
} else {
throw std::invalid_argument("number of x-bins < 0");
}
if (nybins >= 0) {
nYbins = size_t(nybins);
} else {
throw std::invalid_argument("number of y-bins < 0");
}
// Generate mapping of detector/channel IDs to spectrum No
// Detector/channel counter
size_t wi = 0;
// Monitor: IDs start at 1 and increment by 1
for (size_t i = 0; i < nMonitors; i++) {
// std::cout << "SANS instrument monitor number " << i << '\n';
workspace->getSpectrum(wi).setSpectrumNo(specnum_t(wi));
workspace->getSpectrum(wi).setDetectorID(detid_t(wi + 1));
wi++;
}
// Detector pixels
for (size_t ix = 0; ix < nXbins; ix++) {
for (size_t iy = 0; iy < nYbins; iy++) {
workspace->getSpectrum(wi).setSpectrumNo(specnum_t(wi));
workspace->getSpectrum(wi)
.setDetectorID(detid_t(1000000 + iy * 1000 + ix));
wi++;
}
}
}
void SaveCSV::saveXerrors(std::ofstream &stream,
const Mantid::DataObjects::Workspace2D_sptr workspace,
const size_t numberOfHist) {
// If there isn't a dx values present in the first entry then return
if (!workspace->hasDx(0)) {
return;
}
Progress p(this, 0.0, 1.0, numberOfHist);
stream << "\nXERRORS\n";
for (size_t i = 0; i < numberOfHist; i++) {
stream << i;
for (double j : workspace->dx(i)) {
stream << std::setw(15) << j << m_separator;
}
stream << m_lineSeparator;
p.report("Saving x errors...");
}
}
/** Executes the algorithm
*
* @throw runtime_error Thrown if algorithm cannot execute
*/
void Fit1D::exec() {
// Custom initialization
prepare();
// check if derivative defined in derived class
bool isDerivDefined = true;
gsl_matrix *M = NULL;
try {
const std::vector<double> inTest(m_parameterNames.size(), 1.0);
std::vector<double> outTest(m_parameterNames.size());
const double xValuesTest = 0;
JacobianImpl J;
M = gsl_matrix_alloc(m_parameterNames.size(), 1);
J.setJ(M);
// note nData set to zero (last argument) hence this should avoid further
// memory problems
functionDeriv(&(inTest.front()), &J, &xValuesTest, 0);
} catch (Exception::NotImplementedError &) {
isDerivDefined = false;
}
gsl_matrix_free(M);
// Try to retrieve optional properties
int histNumber = getProperty("WorkspaceIndex");
const int maxInterations = getProperty("MaxIterations");
// Get the input workspace
MatrixWorkspace_const_sptr localworkspace = getProperty("InputWorkspace");
// number of histogram is equal to the number of spectra
const size_t numberOfSpectra = localworkspace->getNumberHistograms();
// Check that the index given is valid
if (histNumber >= static_cast<int>(numberOfSpectra)) {
g_log.warning("Invalid Workspace index given, using first Workspace");
histNumber = 0;
}
// Retrieve the spectrum into a vector
const MantidVec &XValues = localworkspace->readX(histNumber);
const MantidVec &YValues = localworkspace->readY(histNumber);
const MantidVec &YErrors = localworkspace->readE(histNumber);
// Read in the fitting range data that we were sent
double startX = getProperty("StartX");
double endX = getProperty("EndX");
// check if the values had been set, otherwise use defaults
if (isEmpty(startX)) {
startX = XValues.front();
modifyStartOfRange(startX); // does nothing by default but derived class may
// provide a more intelligent value
}
if (isEmpty(endX)) {
endX = XValues.back();
modifyEndOfRange(endX); // does nothing by default but derived class may
// previde a more intelligent value
}
int m_minX;
int m_maxX;
// Check the validity of startX
if (startX < XValues.front()) {
g_log.warning("StartX out of range! Set to start of frame.");
startX = XValues.front();
}
// Get the corresponding bin boundary that comes before (or coincides with)
// this value
for (m_minX = 0; XValues[m_minX + 1] < startX; ++m_minX) {
}
// Check the validity of endX and get the bin boundary that come after (or
// coincides with) it
if (endX >= XValues.back() || endX < startX) {
g_log.warning("EndX out of range! Set to end of frame");
endX = XValues.back();
m_maxX = static_cast<int>(YValues.size());
} else {
for (m_maxX = m_minX; XValues[m_maxX] < endX; ++m_maxX) {
}
}
afterDataRangedDetermined(m_minX, m_maxX);
// create and populate GSL data container warn user if l_data.n < l_data.p
// since as a rule of thumb this is required as a minimum to obtained
// 'accurate'
// fitting parameter values.
FitData l_data(this, getProperty("Fix"));
l_data.n =
m_maxX -
m_minX; // m_minX and m_maxX are array index markers. I.e. e.g. 0 & 19.
if (l_data.n == 0) {
g_log.error("The data set is empty.");
throw std::runtime_error("The data set is empty.");
}
if (l_data.n < l_data.p) {
g_log.error(
"Number of data points less than number of parameters to be fitted.");
throw std::runtime_error(
"Number of data points less than number of parameters to be fitted.");
}
l_data.X = new double[l_data.n];
l_data.sigmaData = new double[l_data.n];
l_data.forSimplexLSwrap = new double[l_data.n];
l_data.parameters = new double[nParams()];
// check if histogram data in which case use mid points of histogram bins
const bool isHistogram = localworkspace->isHistogramData();
for (unsigned int i = 0; i < l_data.n; ++i) {
if (isHistogram)
l_data.X[i] =
0.5 * (XValues[m_minX + i] +
XValues[m_minX + i + 1]); // take mid-point if histogram bin
else
l_data.X[i] = XValues[m_minX + i];
}
l_data.Y = &YValues[m_minX];
// check that no error is negative or zero
for (unsigned int i = 0; i < l_data.n; ++i) {
if (YErrors[m_minX + i] <= 0.0) {
l_data.sigmaData[i] = 1.0;
} else
l_data.sigmaData[i] = YErrors[m_minX + i];
}
// create array of fitted parameter. Take these to those input by the user.
// However, for doing the
// underlying fitting it might be more efficient to actually perform the
// fitting on some of other
// form of the fitted parameters. For instance, take the Gaussian sigma
// parameter. In practice it
// in fact more efficient to perform the fitting not on sigma but 1/sigma^2.
// The methods
// modifyInitialFittedParameters() and modifyFinalFittedParameters() are used
// to allow for this;
// by default these function do nothing.
m_fittedParameter.clear();
for (size_t i = 0; i < nParams(); i++) {
m_fittedParameter.push_back(getProperty(m_parameterNames[i]));
}
modifyInitialFittedParameters(
m_fittedParameter); // does nothing except if overwritten by derived class
for (size_t i = 0; i < nParams(); i++) {
l_data.parameters[i] = m_fittedParameter[i];
}
// set-up initial guess for fit parameters
gsl_vector *initFuncArg;
initFuncArg = gsl_vector_alloc(l_data.p);
for (size_t i = 0, j = 0; i < nParams(); i++) {
if (l_data.active[i])
gsl_vector_set(initFuncArg, j++, m_fittedParameter[i]);
}
// set-up GSL container to be used with GSL simplex algorithm
gsl_multimin_function gslSimplexContainer;
gslSimplexContainer.n = l_data.p; // n here refers to number of parameters
gslSimplexContainer.f = &gsl_costFunction;
gslSimplexContainer.params = &l_data;
// set-up GSL least squares container
gsl_multifit_function_fdf f;
f.f = &gsl_f;
f.df = &gsl_df;
f.fdf = &gsl_fdf;
f.n = l_data.n;
f.p = l_data.p;
f.params = &l_data;
// set-up remaining GSL machinery for least squared
const gsl_multifit_fdfsolver_type *T = gsl_multifit_fdfsolver_lmsder;
gsl_multifit_fdfsolver *s = NULL;
if (isDerivDefined) {
s = gsl_multifit_fdfsolver_alloc(T, l_data.n, l_data.p);
gsl_multifit_fdfsolver_set(s, &f, initFuncArg);
}
// set-up remaining GSL machinery to use simplex algorithm
const gsl_multimin_fminimizer_type *simplexType =
gsl_multimin_fminimizer_nmsimplex;
gsl_multimin_fminimizer *simplexMinimizer = NULL;
gsl_vector *simplexStepSize = NULL;
if (!isDerivDefined) {
simplexMinimizer = gsl_multimin_fminimizer_alloc(simplexType, l_data.p);
simplexStepSize = gsl_vector_alloc(l_data.p);
gsl_vector_set_all(simplexStepSize,
1.0); // is this always a sensible starting step size?
gsl_multimin_fminimizer_set(simplexMinimizer, &gslSimplexContainer,
initFuncArg, simplexStepSize);
}
// finally do the fitting
int iter = 0;
int status;
double finalCostFuncVal;
double dof = static_cast<double>(
l_data.n - l_data.p); // dof stands for degrees of freedom
// Standard least-squares used if derivative function defined otherwise
// simplex
Progress prog(this, 0.0, 1.0, maxInterations);
if (isDerivDefined) {
do {
iter++;
status = gsl_multifit_fdfsolver_iterate(s);
if (status) // break if error
break;
status = gsl_multifit_test_delta(s->dx, s->x, 1e-4, 1e-4);
prog.report();
} while (status == GSL_CONTINUE && iter < maxInterations);
double chi = gsl_blas_dnrm2(s->f);
finalCostFuncVal = chi * chi / dof;
// put final converged fitting values back into m_fittedParameter
for (size_t i = 0, j = 0; i < nParams(); i++)
if (l_data.active[i])
m_fittedParameter[i] = gsl_vector_get(s->x, j++);
} else {
do {
iter++;
status = gsl_multimin_fminimizer_iterate(simplexMinimizer);
if (status) // break if error
break;
double size = gsl_multimin_fminimizer_size(simplexMinimizer);
status = gsl_multimin_test_size(size, 1e-2);
prog.report();
} while (status == GSL_CONTINUE && iter < maxInterations);
finalCostFuncVal = simplexMinimizer->fval / dof;
// put final converged fitting values back into m_fittedParameter
for (unsigned int i = 0, j = 0; i < m_fittedParameter.size(); i++)
if (l_data.active[i])
m_fittedParameter[i] = gsl_vector_get(simplexMinimizer->x, j++);
}
modifyFinalFittedParameters(
m_fittedParameter); // do nothing except if overwritten by derived class
// Output summary to log file
std::string reportOfFit = gsl_strerror(status);
g_log.information() << "Iteration = " << iter << "\n"
<< "Status = " << reportOfFit << "\n"
<< "Chi^2/DoF = " << finalCostFuncVal << "\n";
for (size_t i = 0; i < m_fittedParameter.size(); i++)
g_log.information() << m_parameterNames[i] << " = " << m_fittedParameter[i]
<< " \n";
// also output summary to properties
setProperty("OutputStatus", reportOfFit);
setProperty("OutputChi2overDoF", finalCostFuncVal);
for (size_t i = 0; i < m_fittedParameter.size(); i++)
setProperty(m_parameterNames[i], m_fittedParameter[i]);
std::string output = getProperty("Output");
if (!output.empty()) {
// calculate covariance matrix if derivatives available
gsl_matrix *covar(NULL);
std::vector<double> standardDeviations;
std::vector<double> sdExtended;
if (isDerivDefined) {
covar = gsl_matrix_alloc(l_data.p, l_data.p);
gsl_multifit_covar(s->J, 0.0, covar);
int iPNotFixed = 0;
for (size_t i = 0; i < nParams(); i++) {
sdExtended.push_back(1.0);
if (l_data.active[i]) {
sdExtended[i] = sqrt(gsl_matrix_get(covar, iPNotFixed, iPNotFixed));
iPNotFixed++;
}
}
modifyFinalFittedParameters(sdExtended);
for (size_t i = 0; i < nParams(); i++)
if (l_data.active[i])
standardDeviations.push_back(sdExtended[i]);
declareProperty(
new WorkspaceProperty<API::ITableWorkspace>(
"OutputNormalisedCovarianceMatrix", "", Direction::Output),
"The name of the TableWorkspace in which to store the final "
"covariance matrix");
setPropertyValue("OutputNormalisedCovarianceMatrix",
output + "_NormalisedCovarianceMatrix");
Mantid::API::ITableWorkspace_sptr m_covariance =
Mantid::API::WorkspaceFactory::Instance().createTable(
"TableWorkspace");
m_covariance->addColumn("str", "Name");
std::vector<std::string>
paramThatAreFitted; // used for populating 1st "name" column
for (size_t i = 0; i < nParams(); i++) {
if (l_data.active[i]) {
m_covariance->addColumn("double", m_parameterNames[i]);
paramThatAreFitted.push_back(m_parameterNames[i]);
}
}
for (size_t i = 0; i < l_data.p; i++) {
Mantid::API::TableRow row = m_covariance->appendRow();
row << paramThatAreFitted[i];
for (size_t j = 0; j < l_data.p; j++) {
if (j == i)
row << 1.0;
else {
row << 100.0 * gsl_matrix_get(covar, i, j) /
sqrt(gsl_matrix_get(covar, i, i) *
gsl_matrix_get(covar, j, j));
}
}
}
setProperty("OutputNormalisedCovarianceMatrix", m_covariance);
}
declareProperty(new WorkspaceProperty<API::ITableWorkspace>(
"OutputParameters", "", Direction::Output),
"The name of the TableWorkspace in which to store the "
"final fit parameters");
declareProperty(
new WorkspaceProperty<MatrixWorkspace>("OutputWorkspace", "",
Direction::Output),
"Name of the output Workspace holding resulting simlated spectrum");
setPropertyValue("OutputParameters", output + "_Parameters");
setPropertyValue("OutputWorkspace", output + "_Workspace");
// Save the final fit parameters in the output table workspace
Mantid::API::ITableWorkspace_sptr m_result =
Mantid::API::WorkspaceFactory::Instance().createTable("TableWorkspace");
m_result->addColumn("str", "Name");
m_result->addColumn("double", "Value");
if (isDerivDefined)
m_result->addColumn("double", "Error");
Mantid::API::TableRow row = m_result->appendRow();
row << "Chi^2/DoF" << finalCostFuncVal;
for (size_t i = 0; i < nParams(); i++) {
Mantid::API::TableRow row = m_result->appendRow();
row << m_parameterNames[i] << m_fittedParameter[i];
if (isDerivDefined && l_data.active[i]) {
// perhaps want to scale standard deviations with sqrt(finalCostFuncVal)
row << sdExtended[i];
}
}
setProperty("OutputParameters", m_result);
// Save the fitted and simulated spectra in the output workspace
MatrixWorkspace_const_sptr inputWorkspace = getProperty("InputWorkspace");
int iSpec = getProperty("WorkspaceIndex");
const MantidVec &inputX = inputWorkspace->readX(iSpec);
const MantidVec &inputY = inputWorkspace->readY(iSpec);
int histN = isHistogram ? 1 : 0;
Mantid::DataObjects::Workspace2D_sptr ws =
boost::dynamic_pointer_cast<Mantid::DataObjects::Workspace2D>(
Mantid::API::WorkspaceFactory::Instance().create(
"Workspace2D", 3, l_data.n + histN, l_data.n));
ws->setTitle("");
ws->getAxis(0)->unit() =
inputWorkspace->getAxis(0)
->unit(); // UnitFactory::Instance().create("TOF");
for (int i = 0; i < 3; i++)
ws->dataX(i)
.assign(inputX.begin() + m_minX, inputX.begin() + m_maxX + histN);
ws->dataY(0).assign(inputY.begin() + m_minX, inputY.begin() + m_maxX);
MantidVec &Y = ws->dataY(1);
MantidVec &E = ws->dataY(2);
double *lOut =
new double[l_data.n]; // to capture output from call to function()
modifyInitialFittedParameters(m_fittedParameter); // does nothing except if
// overwritten by derived
// class
function(&m_fittedParameter[0], lOut, l_data.X, l_data.n);
modifyInitialFittedParameters(m_fittedParameter); // reverse the effect of
// modifyInitialFittedParameters - if any
for (unsigned int i = 0; i < l_data.n; i++) {
Y[i] = lOut[i];
E[i] = l_data.Y[i] - Y[i];
}
delete[] lOut;
setProperty("OutputWorkspace",
boost::dynamic_pointer_cast<MatrixWorkspace>(ws));
if (isDerivDefined)
gsl_matrix_free(covar);
}
// clean up dynamically allocated gsl stuff
if (isDerivDefined)
gsl_multifit_fdfsolver_free(s);
else {
gsl_vector_free(simplexStepSize);
gsl_multimin_fminimizer_free(simplexMinimizer);
}
delete[] l_data.X;
delete[] l_data.sigmaData;
delete[] l_data.forSimplexLSwrap;
delete[] l_data.parameters;
gsl_vector_free(initFuncArg);
return;
}
void LoadFlexiNexus::load2DWorkspace(NeXus::File *fin) {
Mantid::DataObjects::Workspace2D_sptr ws;
int nSpectra, spectraLength;
std::vector<int> data;
// read the data first
fin->getDataCoerce(data);
Info inf = fin->getInfo();
if (inf.dims.size() == 1) {
nSpectra = 1;
spectraLength = static_cast<int>(inf.dims[0]);
} else {
nSpectra = static_cast<int>(inf.dims[0]);
spectraLength = static_cast<int>(inf.dims[1]);
}
g_log.debug() << "Reading " << nSpectra << " spectra of length "
<< spectraLength << "." << std::endl;
// need to locate x-axis data too.....
std::map<std::string, std::string>::const_iterator it;
std::vector<double> xData;
if ((it = dictionary.find("x-axis")) == dictionary.end()) {
xData.resize(spectraLength);
for (int i = 0; i < spectraLength; i++) {
xData[i] = (double)i;
}
} else {
if (safeOpenpath(fin, it->second)) {
fin->getDataCoerce(xData);
}
}
// need to locate y-axis data too.....
std::vector<double> yData;
if ((it = dictionary.find("y-axis")) == dictionary.end()) {
yData.resize(nSpectra);
for (int i = 0; i < nSpectra; i++) {
yData[i] = (double)i;
}
} else {
if (safeOpenpath(fin, it->second)) {
fin->getDataCoerce(yData);
}
}
// fill the data.......
ws = boost::dynamic_pointer_cast<Mantid::DataObjects::Workspace2D>(
WorkspaceFactory::Instance().create("Workspace2D", nSpectra,
spectraLength, spectraLength));
for (int wsIndex = 0; wsIndex < nSpectra; wsIndex++) {
Mantid::MantidVec &Y = ws->dataY(wsIndex);
for (int j = 0; j < spectraLength; j++) {
Y[j] = data[spectraLength * wsIndex + j];
}
// Create and fill another vector for the errors, containing sqrt(count)
Mantid::MantidVec &E = ws->dataE(wsIndex);
std::transform(Y.begin(), Y.end(), E.begin(), dblSqrt);
ws->setX(wsIndex, xData);
// Xtof ws->getAxis(1)->spectraNo(i)= i;
ws->getSpectrum(wsIndex)
->setSpectrumNo(static_cast<specid_t>(yData[wsIndex]));
ws->getSpectrum(wsIndex)
->setDetectorID(static_cast<detid_t>(yData[wsIndex]));
}
ws->setYUnit("Counts");
// assign an x-axis-name
if ((it = dictionary.find("x-axis-name")) == dictionary.end()) {
const std::string xname("no axis name found");
ws->getAxis(0)->title() = xname;
} else {
const std::string xname(it->second);
ws->getAxis(0)->title() = xname;
if (xname.compare("TOF") == 0) {
g_log.debug() << "Setting X-unit to be TOF" << std::endl;
ws->getAxis(0)->setUnit("TOF");
}
}
addMetaData(fin, ws, (ExperimentInfo_sptr)ws);
// assign the workspace
setProperty("OutputWorkspace", boost::dynamic_pointer_cast<Workspace>(ws));
}